X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 298.0
Details 100 mM Tris-HCl, pH 8.0, 20-35% PEG3350, 3 mM GDP, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 84.03 α = 90
b = 121.04 β = 90
c = 47.82 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2011-07-18
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.9792 APS 24-ID-C

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2.55 44.48 98.0 -- -- -- -- 16553 16222 2.8 2.8 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.55 2.69 86.8 -- -- -- -- --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 2.55 44.48 -- 2.8 15385 15385 814 100.0 -- 0.24296 0.24064 0.28573 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.55 2.617 -- 40 839 0.318 0.383 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 42.266
Anisotropic B[1][1] 1.94
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.49
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.46
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 1.167
r_dihedral_angle_4_deg 20.092
r_dihedral_angle_1_deg 5.523
r_dihedral_angle_3_deg 18.72
r_dihedral_angle_2_deg 36.889
r_bond_refined_d 0.017
r_gen_planes_refined 0.008
r_angle_refined_deg 1.556
r_scbond_it 1.881
r_chiral_restr 0.105
r_scangle_it 3.001
r_mcbond_it 0.646
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3704
Nucleic Acid Atoms 0
Heterogen Atoms 28
Solvent Atoms 64

Software

Software
Software Name Purpose
ADSC data collection version: Quantum
PHENIX model building
REFMAC refinement version: 5.5.0110
XDS data reduction
XDS data scaling
PHENIX phasing